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- PDB-9bgl: Complex of Zinc Finger Antiviral Protein RBD and KHNYN CTD -

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Basic information

Entry
Database: PDB / ID: 9bgl
TitleComplex of Zinc Finger Antiviral Protein RBD and KHNYN CTD
Components
  • Protein KHNYN
  • Zinc finger CCCH-type antiviral protein 1
KeywordsANTIVIRAL PROTEIN / ZINC FINGER ANTIVIRAL PROTEIN / ZAP / RNA BINDING DOMAIN
Function / homology
Function and homology information


positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / negative regulation of viral genome replication / positive regulation of interferon-alpha production / positive regulation of type I interferon production / RNA endonuclease activity / positive regulation of interferon-beta production / response to virus / cytoplasmic ribonucleoprotein granule / Signaling by BRAF and RAF1 fusions ...positive regulation of RIG-I signaling pathway / positive regulation of mRNA catabolic process / negative regulation of viral genome replication / positive regulation of interferon-alpha production / positive regulation of type I interferon production / RNA endonuclease activity / positive regulation of interferon-beta production / response to virus / cytoplasmic ribonucleoprotein granule / Signaling by BRAF and RAF1 fusions / late endosome / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / lysosome / cadherin binding / innate immune response / mRNA binding / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
N4BP1, first type I KH-domain / N4BP1, second type I KH-domain / N4BP1, C-terminal UBA domain / ZAP, zinc finger / ZAP, helix turn helix N-terminal domain / Zap helix turn helix N-terminal domain / Zinc-finger antiviral protein (ZAP) zinc finger domain 3 / WWE domain / : / Ribonuclease Zc3h12a-like, NYN domain ...N4BP1, first type I KH-domain / N4BP1, second type I KH-domain / N4BP1, C-terminal UBA domain / ZAP, zinc finger / ZAP, helix turn helix N-terminal domain / Zap helix turn helix N-terminal domain / Zinc-finger antiviral protein (ZAP) zinc finger domain 3 / WWE domain / : / Ribonuclease Zc3h12a-like, NYN domain / : / Zc3h12a-like Ribonuclease NYN domain / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / K Homology domain, type 1 superfamily / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Protein KHNYN / Zinc finger CCCH-type antiviral protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsMeagher, J.L. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54-AI170660 United States
CitationJournal: Nat Commun / Year: 2024
Title: Functional anatomy of zinc finger antiviral protein complexes.
Authors: Bohn, J.A. / Meagher, J.L. / Takata, M.A. / Goncalves-Carneiro, D. / Yeoh, Z.C. / Ohi, M.D. / Smith, J.L. / Bieniasz, P.D.
History
DepositionApr 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger CCCH-type antiviral protein 1
B: Protein KHNYN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,07610
Polymers32,5632
Non-polymers5138
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.213, 88.001, 94.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zinc finger CCCH-type antiviral protein 1 / ADP-ribosyltransferase diphtheria toxin-like 13 / ARTD13 / Inactive Poly [ADP-ribose] polymerase 13 ...ADP-ribosyltransferase diphtheria toxin-like 13 / ARTD13 / Inactive Poly [ADP-ribose] polymerase 13 / PARP13 / Zinc finger CCCH domain-containing protein 2 / Zinc finger antiviral protein / ZAP


Mass: 25991.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZC3HAV1, ZC3HDC2, PRO1677 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z2W4
#2: Protein Protein KHNYN / KH and NYN domain-containing protein


Mass: 6571.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHNYN, KIAA0323 / Production host: Escherichia coli (E. coli) / References: UniProt: O15037
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Aug 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.294→50 Å / Num. obs: 14154 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Χ2: 0.857 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.347.20.5486850.9030.9740.2190.5910.846100
2.34-2.387.30.4947040.9180.9780.1960.5320.859100
2.38-2.437.30.4427020.9430.9850.1740.4760.877100
2.43-2.487.40.4486680.960.990.1760.4820.86100
2.48-2.537.30.3487020.960.990.1370.3740.885100
2.53-2.597.30.2947170.9660.9910.1160.3160.885100
2.59-2.667.30.2636590.9760.9940.1040.2830.913100
2.66-2.737.30.2197040.9820.9950.0870.2360.904100
2.73-2.817.30.1886990.9880.9970.0750.2030.919100
2.81-2.97.30.1556890.9910.9980.0610.1660.906100
2.9-37.30.1257020.9930.9980.050.1340.953100
3-3.127.30.1096950.9930.9980.0430.1170.937100
3.12-3.267.20.0897200.9930.9980.0350.0960.98100
3.26-3.447.20.086900.9960.9990.0320.0861.06100
3.44-3.657.10.0667190.9950.9990.0270.0721.121100
3.65-3.937.10.0537060.9970.9990.0210.0570.879100
3.93-4.337.10.0427200.99810.0170.0450.674100
4.33-4.956.90.0357300.99810.0140.0380.54899.9
4.95-6.246.90.0367420.99810.0150.0390.505100
6.24-446.10.0418010.9970.9990.0180.0450.60899.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.294→44 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.387 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 680 5.06 %RANDOM
Rwork0.2062 ---
obs0.2082 13430 94.8 %-
Displacement parametersBiso mean: 39.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.7316 Å20 Å20 Å2
2---1.4744 Å20 Å2
3---0.7428 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.294→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 17 131 2223
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072129HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.852865HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d770SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes368HARMONIC5
X-RAY DIFFRACTIONt_it2129HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion16.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion273SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance20HARMONIC1
X-RAY DIFFRACTIONt_utility_angle30HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1680SEMIHARMONIC4
LS refinement shellResolution: 2.294→2.33 Å
RfactorNum. reflection% reflection
Rfree0.2806 -3.29 %
Rwork0.2191 382 -
obs--66.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54510.9238-0.49964.3942-0.77911.0871-0.1290.19910.01170.06740.23540.04370.0809-0.1504-0.1064-0.0610.0040.0203-0.03570.0335-0.01314.042-14.7005-17.5129
25.74290.3743-2.48936.1956-2.47233.8321-0.37320.33790.201-0.81660.5618-0.5170.1546-0.0012-0.1886-0.1048-0.10590.168-0.05080.02350.1121.22132.5792-29.9772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|0 - 224}
2X-RAY DIFFRACTION2{B|669 - 719}

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